Novel Single-Nucleotide Polymorphisms (SNPs) and Genetic Studies of the Shadow of Prion Protein (SPRN) in Quails

Abstract

Prion diseases are a group of deadly neurodegenerative disorders caused by the accumulation of the normal prion protein (PrP^C) into misfolding pathological conformations (PrP^Sc). The PrP gene is essential for the development of prion diseases. Another candidate implicated in prion pathogenesis is the shadow of the prion protein (<i>SPRN</i>) gene. To date, genetic polymorphisms of the <i>SPRN</i> gene and the structure of the Sho protein have not been explored in quails. We used polymerase chain reaction (PCR) to amplify the <i>SPRN</i> gene sequence and then conducted Sanger DNA sequencing to identify the genetic polymorphisms in quail <i>SPRN</i>. Furthermore, we examined the genotype, allele, and haplotype frequencies, and assessed the linkage disequilibrium among the genetic polymorphisms of the <i>SPRN</i> gene in quails. Additionally, we used <i>in silico</i> programs such as MutPred2, SIFT, MUpro, AMYCO, and SODA to predict the pathogenicity of non-synonymous single-nucleotide polymorphisms (SNPs). Alphafold2 predicted the 3D structure of the Sho protein in quails. The results showed that a total of 13 novel polymorphisms were found in 106 quails, including 4 non-synonymous SNPs. Using SIFT and MUpro <i>in silico</i> programs, three out of the four non-synonymous SNPs (A68T, L74P, and M105I) were predicted to have deleterious effects on quail Sho. Furthermore, the 3D structure of quail Sho was predicted to be similar to that of chicken Sho. To our knowledge, this is the first report to investigate the genetic and structural properties of the quail <i>SPRN</i> gene.